Evaluate gene sets by cell type-specific gene expression
Wei Sun
2024-07-04
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 16.00 17.00 18.00 17.85 18.00 19.00## [1] 40## [1] 16 17 17 17 17 17 17 17 17 17 17 17 18 18 18 18 18 18 18 18 18 18 18 18 18
## [26] 18 18 18 18 18 18 18 18 19 19 19 19 19 19 19Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"##
## FALSE TRUE
## 1607 42##
## FALSE TRUE <NA>
## 42 1565 42gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: C10orf91 LINC02870
## 2: C12orf10 MYG1
## 3: C12orf45 NOPCHAP1
## 4: C6orf48 SNHG32
## 5: C6orf99 LINC02901
## 6: CXorf40A EOLA1
## 7: CXorf57 RADX
## 8: FAM102A EEIG1
## 9: FAM173A ANTKMT
## 10: FAM213B PRXL2B
## 11: H2AFX H2AX
## 12: HIST1H2AG H2AC11
## 13: HIST1H2BK H2BC12
## 14: HIST1H2BN H2BC15
## 15: HIST1H3A H3C1
## 16: HIST1H3H H3C10
## 17: HIST1H4C H4C3
## 18: HIST2H2BF H2BC18
## 19: KIAA0391 PRORP
## 20: QARS EPRS1
## 21: SEPT6 SEPTIN6
## 22: ARNTL BMAL1
## 23: C12orf65 MTRFR
## 24: C16orf72 HAPSTR1
## 25: CCDC84 CENATAC
## 26: DOPEY2 DOP1B
## 27: FAM126B HYCC2
## 28: FAM160B1 FHIP2A
## 29: H1FX H1-10
## 30: H2AFJ H2AJ
## 31: HEXDC HEXD
## 32: HIST1H1C H1-2
## 33: HIST1H1D H1-3
## 34: HIST1H1E H1-4
## 35: KIAA1109 BLTP1
## 36: KIAA1551 RESF1
## 37: MKL1 MRTFA
## 38: NARFL CIAO3
## 39: SEPT2 SEPTIN6
## 40: TARSL2 TARS3
## 41: TMEM8A PGAP6
## 42: WDR60 DYNC2I1
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 1649 3## sym_in_data sym_limma gene_symbol
## 1: ABLIM1 ABLIM1 ABLIM1
## 2: AC004687.1 <NA> AC004687.1
## 3: AC004854.2 <NA> AC004854.2
## 4: AC007384.1 <NA> AC007384.1
## 5: AC007952.4 <NA> AC007952.4## t1
## 1 2
## 1647 1## sym_in_data sym_limma gene_symbol
## 1: SEPT6 SEPTIN6 SEPTIN6
## 2: SEPT2 SEPTIN6 SEPTIN6Read in cell type-specific expression data
Cell type specific gene expression were downloaded from protein atlas.
## [1] 1587110 4## Gene Gene name Cell type nTPM
## 1: ENSG00000000003 TSPAN6 Adipocytes 149.5
## 2: ENSG00000000003 TSPAN6 Alveolar cells type 1 6.1
## 3: ENSG00000000003 TSPAN6 Alveolar cells type 2 10.5
## 4: ENSG00000000003 TSPAN6 Astrocytes 13.9
## 5: ENSG00000000003 TSPAN6 B-cells 1.5## [1] 79##
## Adipocytes Alveolar cells type 1
## 20090 20090
## Alveolar cells type 2 Astrocytes
## 20090 20090
## B-cells Basal keratinocytes
## 20090 20090
## Basal prostatic cells Basal respiratory cells
## 20090 20090
## Basal squamous epithelial cells Bipolar cells
## 20090 20090
## Breast glandular cells Breast myoepithelial cells
## 20090 20090
## Cardiomyocytes Cholangiocytes
## 20090 20090
## Club cells Collecting duct cells
## 20090 20090
## Cone photoreceptor cells Cytotrophoblasts
## 20090 20090
## dendritic cells Distal enterocytes
## 20090 20090
## Distal tubular cells Ductal cells
## 20090 20090
## Early spermatids Endometrial ciliated cells
## 20090 20090
## Endometrial stromal cells Endothelial cells
## 20090 20090
## Enteroendocrine cells Erythroid cells
## 20090 20090
## Excitatory neurons Exocrine glandular cells
## 20090 20090
## Extravillous trophoblasts Fibroblasts
## 20090 20090
## Gastric mucus-secreting cells Glandular and luminal cells
## 20090 20090
## granulocytes Granulosa cells
## 20090 20090
## Hepatocytes Hofbauer cells
## 20090 20090
## Horizontal cells Inhibitory neurons
## 20090 20090
## Intestinal goblet cells Ionocytes
## 20090 20090
## Kupffer cells Langerhans cells
## 20090 20090
## Late spermatids Leydig cells
## 20090 20090
## Macrophages Melanocytes
## 20090 20090
## Microglial cells monocytes
## 20090 20090
## Mucus glandular cells Muller glia cells
## 20090 20090
## NK-cells Oligodendrocyte precursor cells
## 20090 20090
## Oligodendrocytes Pancreatic endocrine cells
## 20090 20090
## Paneth cells Peritubular cells
## 20090 20090
## Plasma cells Prostatic glandular cells
## 20090 20090
## Proximal enterocytes Proximal tubular cells
## 20090 20090
## Respiratory ciliated cells Rod photoreceptor cells
## 20090 20090
## Salivary duct cells Schwann cells
## 20090 20090
## Serous glandular cells Sertoli cells
## 20090 20090
## Skeletal myocytes Smooth muscle cells
## 20090 20090
## Spermatocytes Spermatogonia
## 20090 20090
## Squamous epithelial cells Suprabasal keratinocytes
## 20090 20090
## Syncytiotrophoblasts T-cells
## 20090 20090
## Theca cells Thymic epithelial cells
## 20090 20090
## Undifferentiated cells
## 20090## [1] 602700 5## Gene Gene name Immune cell TPM pTPM
## 1: ENSG00000000003 TSPAN6 basophil NA 1.2
## 2: ENSG00000000003 TSPAN6 Central memory CD8 T-cell NA 1.7
## 3: ENSG00000000003 TSPAN6 classical monocyte NA 0.2
## 4: ENSG00000000003 TSPAN6 Effector memory CD8 T-cell NA 0.7
## 5: ENSG00000000003 TSPAN6 Exhausted memory B-cell NA 0.7## Mode NA's
## logical 602700## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 0.00 3.10 49.74 27.20 96572.50## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.10 1.70 11.60 67.96 42.80 96572.50## [1] 30##
## basophil Central memory CD8 T-cell
## 20090 20090
## classical monocyte Effector memory CD8 T-cell
## 20090 20090
## Exhausted memory B-cell intermediate monocyte
## 20090 20090
## MAIT T-cell Memory CD4 T-cell TFH
## 20090 20090
## Memory CD4 T-cell Th1 Memory CD4 T-cell Th1/Th17
## 20090 20090
## Memory CD4 T-cell Th17 Memory CD4 T-cell Th2
## 20090 20090
## myeloid DC naive B-cell
## 20090 20090
## naive CD4 T-cell naive CD8 T-cell
## 20090 20090
## neutrophil NK-cell
## 20090 20090
## non-classical monocyte Non-switched memory B-cell
## 20090 20090
## Non-Vd2 gdTCR Plasmablast
## 20090 20090
## plasmacytoid DC Progenitor cell
## 20090 20090
## Switched memory B-cell T-reg
## 20090 20090
## Terminal effector memory CD4 T-cell Terminal effector memory CD8 T-cell
## 20090 20090
## total PBMC Vd2 gdTCR
## 20090 20090## [1] 30 2## Cell_type Lineage
## 1: Basophil Granulocytes
## 2: Neutrophil GranulocytesCheck gene expression for each gene set
## [1] 1649 3for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]
n_genes = sum(genes %in% ct_immune$`Gene name`)
print(sprintf("found %d genes.", n_genes))
if(n_genes == 0) { next }
df = ct_immune[`Gene name` %in% genes,]
dim(df)
df[1:2,]
stopifnot(all(str_to_lower(df$`Immune cell`) %in%
str_to_lower(lineage$Cell_type)))
mat1 = match(str_to_lower(df$`Immune cell`),
str_to_lower(lineage$Cell_type))
df = cbind(df, lineage[mat1,])
df[1:2,]
df$Cell_type = factor(df$Cell_type, levels = lineage$Cell_type)
df = df[df$Lineage != "Total PBMC",]
df$Lineage = factor(df$Lineage,
levels = setdiff(lineage$Lineage, "Total PBMC"))
p1 = ggplot(df, aes(x=Cell_type, y=log10(pTPM + 0.1), fill=Lineage)) +
geom_boxplot() + xlab("Cell type") + ggtitle(set_k) +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
scale_fill_brewer(palette="RdBu")
print(p1)
}## [1] 1
## [1] "ARHGEF3" "ARL4C" "BROX" "COL6A2" "COL6A3" "DMTF1"
## [7] "ELMOD3" "FAM169A" "GPR174" "IFITM2" "LAIR2" "LINC02256"
## [13] "PIK3CD" "PIK3R5" "RUBCN" "SLCO3A1" "SUSD6" "TRGV10"
## [19] "XCL1"
## [1] "found 18 genes."
## [1] 2
## [1] "ISCA1" "LCP2" "NSUN6" "NT5E" "SLC27A5" "TRAT1"
## [7] "AFF1" "AFF4" "COX19" "ITK" "LONP2" "MYO9A"
## [13] "PNPLA8" "TBC1D14" "TRAPPC11" "TRAPPC8" "TRAPPC9" "ZNF557"
## [1] "found 18 genes."
## [1] 3
## [1] "CAMK4" "CCNB1IP1" "CMTM7" "EPHX2" "HDHD3" "HIBADH"
## [7] "LBH" "MZT2A" "PCMTD2" "PDE7A" "SNHG15" "TC2N"
## [13] "THEM4" "ZFAS1" "CD46" "FAM126B" "KLF3" "VPS13A"
## [1] "found 15 genes."
## [1] 4
## [1] "CREBL2" "DYRK4" "IGKV3-20" "MZF1" "NBPF14" "TBCCD1"
## [7] "TRAV13-1" "TRAV8-3" "TRGV5" "TSPYL4" "CYTOR" "IQCG"
## [13] "PATL2" "PYROXD1" "SENP7" "TRIM38" "TSPAN32" "ZNF683"
## [1] "found 17 genes."
## [1] 5
## [1] "CCR7" "TRABD2A" "AC116407.2" "DOCK10" "HRH2"
## [6] "LINC02446" "MX2" "OAS2" "OXNAD1" "PCED1B"
## [11] "S100A12" "TRAV12-3" "TRAV19" "TRAV27" "TRAV4"
## [16] "TRAV9-2" "TRBV11-2" "TRBV4-2"
## [1] "found 15 genes."
## [1] 6
## [1] "BBS9" "COG5" "DTHD1" "KLRF1" "LRRC23" "MAP3K2"
## [7] "MTRNR2L8" "NT5C3B" "TOX" "TRAV3" "TRBV7-2" "TRGV8"
## [13] "ZNF862" "COG7" "MCTP2" "MYBL1" "TRGC2"
## [1] "found 17 genes."
## [1] 7
## [1] "CST3" "APOL6" "CD226" "DIAPH2" "DOCK11" "EPSTI1" "ERAP2"
## [8] "GNPTAB" "GPR141" "LILRB1" "MIGA1" "OGA" "PARP15" "PTPRJ"
## [15] "ST6GAL1" "TTC17" "UNC13D" "ZNF493"
## [1] "found 18 genes."
## [1] 8
## [1] "ARMH1" "BTG1" "IL6R" "SLC2A3" "TMIGD2" "ARHGAP45"
## [7] "DDIT4" "HEXDC" "IL6ST" "ITM2A" "OSM" "PPP4R3B"
## [13] "PSMA3-AS1" "STK17B" "TARSL2" "TENT5C" "Z93930.2" "ZC3H7B"
## [1] "found 16 genes."
## [1] 9
## [1] "ALOX5AP" "FCRL3" "GCSAM" "GTF3A" "ICAM3" "MFNG"
## [7] "TRBC1" "ADGRE5" "ARHGAP30" "CCL4" "CD38" "CTSW"
## [13] "FCRL6" "FGFBP2" "SLA2" "TBC1D2B" "TRBC2" "ZAP70"
## [19] "ZNF276"
## [1] "found 19 genes."
## [1] 10
## [1] "ANKRD49" "ATAD2B" "CCNH" "CES1" "CLUH" "FAM13B"
## [7] "GPATCH2L" "INO80D" "MICAL2" "MX1" "NAA25" "NARFL"
## [13] "NLRC5" "PARP9" "RHOH" "STAT4" "SYNRG"
## [1] "found 17 genes."
## [1] 11
## [1] "AC027644.3" "AC087623.3" "AC119396.1" "AC245297.3" "ARRDC2"
## [6] "IER5" "KLF10" "KMT2E-AS1" "LINC00649" "RAB33B"
## [11] "SDR42E2" "SESN2" "TCP11L2" "WARS2" "MARF1"
## [16] "RUFY2" "SZT2" "XIST"
## [1] "found 11 genes."
## [1] 12
## [1] "ASL" "GALNT11" "NXT2" "ASCL2" "BTN3A1" "FRYL" "GNLY"
## [8] "GON4L" "HSH2D" "INPP4A" "PHF14" "POLH" "RALGAPB" "SEMA4D"
## [15] "TAOK1" "TAOK3" "USP16" "ZEB2"
## [1] "found 18 genes."
## [1] 13
## [1] "AL118516.1" "AL451085.1" "AL627171.1" "ATP2B1-AS1" "HELQ"
## [6] "INPP4B" "LINC02273" "NUP58" "PRR7" "PTGER4"
## [11] "RGS1" "AC016831.7" "CEMIP2" "CRYBG1" "GDPD5"
## [16] "PRR5L" "THUMPD3-AS1" "TMEM131L"
## [1] "found 11 genes."
## [1] 14
## [1] "RELT" "B4GALT1" "CAPNS1" "CROCC" "CST7" "CX3CR1"
## [7] "DDHD1" "IL2RG" "IRAK4" "LINC02384" "MBP" "RNF213"
## [13] "SAMD9L" "SPN" "SYNE1" "UBE2H" "UBR2"
## [1] "found 16 genes."
## [1] 15
## [1] "CYB5D2" "INTS6" "INTS8" "PASK" "PITPNC1" "TMEM134" "TRG-AS1"
## [8] "CCDC88C" "EFHD2" "GZMA" "GZMH" "NEAT1" "PEX1" "PEX26"
## [15] "PRR14L" "SSH1" "STK10"
## [1] "found 15 genes."
## [1] 16
## [1] "AC004854.2" "AC083798.2" "AK5" "CD40LG" "CITED2"
## [6] "EI24" "FAM213B" "FXYD7" "MYLIP" "NR1D1"
## [11] "PIK3IP1" "PPP1R15B" "RGL4" "SLC38A2" "TESPA1"
## [16] "WDR86" "WSB1" "ARRDC3" "ITPR2"
## [1] "found 17 genes."
## [1] 17
## [1] "ABCA5" "AC020659.1" "ADHFE1" "CCDC84" "CLEC16A"
## [6] "CPPED1" "DDX60L" "GABPB2" "GCN1" "HECTD4"
## [11] "ISG20" "LAG3" "ODF3B" "PDZD4" "TMEM127"
## [16] "TRAC" "VTI1A" "ZCCHC2"
## [1] "found 17 genes."
## [1] 18
## [1] "AHCTF1" "CAPN15" "CCDC112" "DOPEY2" "H6PD" "HLA-DPB1"
## [7] "HLA-DQA1" "KLHDC4" "N4BP1" "PNPLA6" "PREX1" "PTGDS"
## [13] "RREB1" "SLC38A10" "TBC1D9B" "ZNF292" "ZNF318"
## [1] "found 17 genes."
## [1] 19
## [1] "C12orf45" "CLDND1" "CXXC5" "GSTM1" "ITGAE" "KCTD7"
## [7] "KLRK1" "MSC" "NCR1" "PAPSS1" "RHOC" "SESN1"
## [13] "ARAP2" "GALNT3" "HIVEP3" "NLRC3" "SLF2" "ZDHHC5"
## [1] "found 17 genes."
## [1] 20
## [1] "HMBOX1" "KIF9" "ABCA7" "ANKRD36" "AP3B1" "AP3M2" "ARHGEF9"
## [8] "C2CD3" "C5orf24" "GPHN" "PIP4K2B" "RIPOR2" "UVRAG" "VPS18"
## [15] "VPS39" "WDR60" "XPO6" "ZBTB20" "ZNF407"
## [1] "found 19 genes."
## [1] 21
## [1] "GADD45B" "TRBV6-1" "AKNA" "DENND4B" "FAM78A"
## [6] "GPR132" "HPS4" "MT2A" "NBEAL2" "NUTM2B-AS1"
## [11] "PCNX1" "PUM3" "SEC14L1" "SLC16A1-AS1" "TRANK1"
## [16] "TRBV2" "TRGV4" "TTC38" "ZNF83"
## [1] "found 17 genes."
## [1] 22
## [1] "AC044849.1" "APMAP" "C10orf91" "MATK" "BICRAL"
## [6] "ERBIN" "GZMB" "ITGAL" "KIAA2026" "MYO1G"
## [11] "NKG7" "RAP1GAP2" "RASGRP1" "RNF125" "RNF19A"
## [16] "SPON2" "SRGN" "VPS13C"
## [1] "found 16 genes."
## [1] 23
## [1] "AMD1" "CCNL1" "GLTP" "NT5DC1" "RGCC" "RSRP1"
## [7] "SERINC5" "SNHG12" "ANKRD36B" "ANKRD36C" "CHD9" "EML4"
## [13] "ENOSF1" "NFATC3" "PARP4" "SLFN12L" "TEP1" "TTC14"
## [19] "ZNF708"
## [1] "found 18 genes."
## [1] 24
## [1] "AC008555.5" "AL135791.1" "BTG2" "CXorf40A" "LIME1"
## [6] "LINC00402" "MCUB" "PDCD4-AS1" "PGGHG" "PRAG1"
## [11] "TNFRSF25" "TRAV14DV4" "ZNF749" "CARD16" "GK5"
## [16] "MIAT" "PCSK7" "SPATA13"
## [1] "found 12 genes."
## [1] 25
## [1] "CSRNP1" "ID1" "TXK" "ZC3H12A" "ARID5B" "CISH" "EHBP1L1"
## [8] "FGL2" "GBP1" "GBP5" "KLF6" "MKL1" "NFKBIZ" "PIM1"
## [15] "PLAC8" "RIC3" "SETD5"
## [1] "found 17 genes."
## [1] 26
## [1] "ABR" "ARAP1" "C16orf72" "CHD6" "CREBZF" "DUS1L"
## [7] "FAM53B" "HECA" "HERC3" "HERC6" "INPP5D" "LY6E"
## [13] "PARP11" "RAB27B" "SYTL3" "TTC16" "XAF1" "ZNF652"
## [1] "found 17 genes."
## [1] 27
## [1] "CD27" "CD28" "COA1" "COQ8A" "CRLF3" "CYB561A3"
## [7] "GZMK" "IER3" "KLRG1" "LEPROTL1" "RCSD1" "RTRAF"
## [13] "SLC38A1" "STK17A" "TMEM107" "TMEM42" "ZFAND1" "RFWD3"
## [1] "found 18 genes."
## [1] 28
## [1] "AIF1" "ANXA2R" "BEX4" "CHRM3-AS2" "EPS8" "RCAN3"
## [7] "SELL" "TCEA3" "CASP10" "CHD1" "CYTH1" "MIDN"
## [13] "MSI2" "RNF157" "SCRN3" "SOS1" "VCAN"
## [1] "found 16 genes."
## [1] 29
## [1] "AOAH" "CARHSP1" "EOMES" "GIMAP1" "GSTM4" "ADGRG1"
## [7] "DGKD" "IGKV3-15" "IRF9" "ITGAM" "KIR2DL3" "MYO1F"
## [13] "NCKAP1L" "NECAP1" "PRKCH" "SLFN5" "TUT7" "YPEL1"
## [1] "found 18 genes."
## [1] 30
## [1] "AC007384.1" "AC015982.1" "CCL4L2" "MZF1-AS1" "RETREG1"
## [6] "ABCC10" "AC092683.1" "AP005482.1" "BMT2" "FAM133B"
## [11] "GRK2" "MINDY2" "POLR2J3-1" "SIDT1" "THAP5"
## [16] "TRDC" "TRDV1" "XCL2" "ZNF808"
## [1] "found 13 genes."
## [1] 31
## [1] "AC004687.1" "AC007952.4" "AC025164.1" "AC025171.3" "AC087239.1"
## [6] "AC245014.3" "AL121944.1" "AL139246.5" "CRTAM" "ILF3-DT"
## [11] "JAML" "NR4A3" "SNHG8" "SNHG9" "TRAV12-2"
## [16] "TRBV3-1" "TRBV6-2" "TRBV7-9"
## [1] "found 7 genes."
## [1] 32
## [1] "ADCY7" "BCL9L" "CELF2" "CHST12" "ETNK1" "GALNT2"
## [7] "KCNAB2" "KIAA1109" "KIAA1551" "KLF2" "MPPE1" "PLEK"
## [13] "PRDM2" "PTPN7" "SUSD1" "UGGT1" "WDTC1" "ZBP1"
## [1] "found 17 genes."
## [1] 33
## [1] "CD84" "CMC1" "FAM118A" "GLA" "HIKESHI"
## [6] "HLA-DMB" "KIR3DL2" "KLRC3" "LETMD1" "MAPRE2"
## [11] "SH2D1A" "TRAV38-2DV8" "TRBV6-5" "TRGV9" "MCOLN2"
## [16] "TMEM181"
## [1] "found 16 genes."
## [1] 34
## [1] "GATA3" "GPR183" "MAP3K8" "NR4A2" "SLC4A4" "TIGIT"
## [7] "ARHGAP10" "CSNK1G2" "FAM160B1" "GPRIN3" "LPCAT1" "LRRC8A"
## [13] "PARP14" "RAPGEF1" "SLC20A1" "TBX21" "TGFBR3" "ZFAND3"
## [1] "found 17 genes."
## [1] 35
## [1] "ALKBH7" "ARL4A" "ATP5F1A" "C6orf48" "EFCAB2" "FAM173A" "FCMR"
## [8] "MPST" "NOSIP" "PTRHD1" "RGS10" "ELMO1" "IQGAP2" "LPIN1"
## [15] "PDE4B" "PDE4D" "TOB1" "TUT4"
## [1] "found 17 genes."
## [1] 36
## [1] "AC012645.3" "AC016405.3" "AC020911.2" "AC083880.1" "AC091271.1"
## [6] "AC103591.3" "AF213884.3" "AL357060.1" "ARF4-AS1" "C6orf99"
## [11] "CSKMT" "HIPK1-AS1" "INTS6L" "KCNQ1OT1" "LINC01465"
## [16] "NPIPB4" "OSER1-DT" "Z93241.1"
## [1] "found 3 genes."
## [1] 37
## [1] "BNIP3L" "MXI1" "NUAK2" "PDE3B" "GALNT10" "HIPK1" "IFI44L"
## [8] "MBD5" "NRDC" "PPM1K" "RASA3" "RLF" "SETX" "TMEM8A"
## [15] "TRBV7-6" "VPS13B" "VPS13D"
## [1] "found 17 genes."
## [1] 38
## [1] "AL138963.3" "IGLV1-44" "LRRN3" "LST1" "MATR3-1"
## [6] "NOCT" "THAP9-AS1" "TRAV1-2" "TRAV21" "TRAV5"
## [11] "TRAV8-4" "TRBV20-1" "TRBV28" "TRBV9" "TRGV7"
## [16] "VAMP7" "IFI27"
## [1] "found 13 genes."
## [1] 39
## [1] "C12orf10" "COQ7" "CXorf57" "EPB41L4A-AS1" "FAM102A"
## [6] "HIST1H3H" "IFRD1" "LDLRAP1" "LTB" "NELL2"
## [11] "TCF7" "TMEM204" "ZNF10" "ZNF575" "MAPK8IP3"
## [16] "USP34" "ZBTB40"
## [1] "found 15 genes."
## [1] 40
## [1] "AL136454.1" "BX284668.6" "TRAV8-2" "DDX3Y" "EIF1AY"
## [6] "ETFDH" "KDM5D" "MAF" "MTERF2" "RPAP1"
## [11] "RPS4Y1" "SBNO2" "TRAV17" "TTTY15" "UTY"
## [16] "ZMIZ2" "ZNF236"
## [1] "found 14 genes."
Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 4179730 223.3 11673970 623.5 NA 11673970 623.5
## Vcells 20591749 157.2 61723001 471.0 65536 61693859 470.7## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] stringr_1.5.0 limma_3.54.2 tidyr_1.3.0 ggpubr_0.6.0
## [5] ggplot2_3.4.2 data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.10 png_0.1-8 Biostrings_2.66.0
## [4] digest_0.6.31 utf8_1.2.3 R6_2.5.1
## [7] GenomeInfoDb_1.34.9 backports_1.4.1 stats4_4.2.3
## [10] RSQLite_2.3.1 evaluate_0.20 httr_1.4.6
## [13] pillar_1.9.0 zlibbioc_1.44.0 rlang_1.1.0
## [16] rstudioapi_0.14 car_3.1-2 jquerylib_0.1.4
## [19] blob_1.2.4 R.oo_1.25.0 R.utils_2.12.2
## [22] S4Vectors_0.36.2 rmarkdown_2.21 labeling_0.4.2
## [25] RCurl_1.98-1.12 bit_4.0.5 munsell_0.5.0
## [28] broom_1.0.4 compiler_4.2.3 xfun_0.39
## [31] pkgconfig_2.0.3 BiocGenerics_0.44.0 htmltools_0.5.5
## [34] tidyselect_1.2.0 KEGGREST_1.38.0 GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1 IRanges_2.32.0 fansi_1.0.4
## [40] crayon_1.5.2 dplyr_1.1.2 withr_2.5.0
## [43] R.methodsS3_1.8.2 bitops_1.0-7 grid_4.2.3
## [46] jsonlite_1.8.4 gtable_0.3.3 lifecycle_1.0.3
## [49] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
## [52] cli_3.6.1 stringi_1.7.12 cachem_1.0.7
## [55] carData_3.0-5 farver_2.1.1 XVector_0.38.0
## [58] ggsignif_0.6.4 bslib_0.4.2 generics_0.1.3
## [61] vctrs_0.6.2 RColorBrewer_1.1-3 org.Hs.eg.db_3.16.0
## [64] tools_4.2.3 bit64_4.0.5 Biobase_2.58.0
## [67] glue_1.6.2 purrr_1.0.1 abind_1.4-5
## [70] fastmap_1.1.1 yaml_2.3.7 AnnotationDbi_1.60.2
## [73] colorspace_2.1-0 rstatix_0.7.2 memoise_2.0.1
## [76] knitr_1.44 sass_0.4.5